AMBER Archive (2004)

Subject: AMBER: ligand minimization

From: atobak_at_eden.rutgers.edu
Date: Sat May 08 2004 - 16:13:21 CDT

Hello amber users,

I'm trying to calculate the binding energies of several compounds to a
certain gasteiger-charged receptor. After running sander, the energies
of the complex, ligand, receptor, the ligand + receptor, and binding are
as follows (respectively):

 -8517.2319 0.0000 -8516.9491 -8516.9491 -0.2828
 -8517.2319 0.0000 -8516.9491 -8516.9491 -0.2828
 -8517.2319 0.0000 -8516.9491 -8516.9491 -0.2828

It's clear that I'm having trouble calculating my ligand energies, but
I'm not sure why. Below is a ligand output file. I don't know what the
%FORMAT error means or how to fix it.

Can you help? I'm working with Amber 7 on a Dell Linux machine.

Thank you!
Anne

          -------------------------------------------------------
          Amber 7 SANDER Scripps/UCSF 2002
          -------------------------------------------------------

| Sat May 8 16:39:05 2004

  [-O]verwriting output

File Assignments:
| MDIN: no_min_gb.in
| MDOUT: gb_l/30.out
|INPCRD: gb_l/30.crd
| PARM: gb_l/30.top
|RESTRT: gb_l/30.rst
| REFC: gb_l/30.crd
| MDVEL: mdvel
| MDEN: mden
| MDCRD: mdcrd
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip

 Here is the input file:

 &cntrl
   imin=0,
   cut=200.0, igb=1, saltcon=0.2, gbsa=1,
   ntpr=20, ntx=1, ntb=0,
   ntr=0,
 &end

--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags:
| New format PARM file being parsed.
| Version = 1.000 Date = 05/08/04 Time = 16:38:20
 NATOM = 0 NTYPES = 0 NBONH = 0 MBONA = 0
 NTHETH = 0 MTHETA = 0 NPHIH = 0 MPHIA = 0
 NHPARM = 0 NPARM = 0 NNB = 0 NRES = 0
 NBONA = 0 NTHETA = 0 NPHIA = 0 NUMBND = 0
 NUMANG = 0 NPTRA = 0 NATYP = 0 NPHB = 0
 IFBOX = 0 NMXRS = 0 IFCAP = 0 NEXTRA = 0

| Memory Use Allocated Used
| Real 4000000 91
| Hollerith 400000 2
| Integer 4000000 10004
ERROR: No %FORMAT field found following flag "ANGLES_INC_HYDROGEN"

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